Contacts of the strand formed by residues 162 - 168 (chain B) in PDB entry 1QQG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B ASN* 3.9 7.5 - - - +
75B ARG* 2.9 33.9 + - - -
160B PHE* 3.6 1.6 - - - +
161B LYS* 1.3 90.5 - - + +
163B VAL* 1.3 70.4 + - - +
164B TRP* 3.3 36.0 - - + -
185B LEU 4.3 0.9 - - - -
187B LEU* 2.8 35.6 + - + -
248B ASN* 5.9 1.1 - - - -
252B THR* 3.8 17.4 - - + +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B PHE* 4.0 15.3 - - + -
71B ASN* 3.3 34.3 - - + +
73B ASN* 3.5 2.6 - - - +
75B ARG* 2.6 26.8 + - - +
87B TYR* 3.2 41.0 + - + -
160B PHE* 3.9 17.7 - - + -
162B GLU* 1.3 82.0 - - - +
164B TRP* 1.3 61.0 - - - +
184B ARG* 3.8 17.7 - - + -
185B LEU 3.3 3.8 - - - -
186B CYS* 4.2 8.1 - - - -
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Residues in contact with TRP 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ARG* 3.2 35.6 - - - +
87B TYR* 4.3 2.9 - - - -
162B GLU* 3.3 38.8 - - + -
163B VAL* 1.3 73.1 - - - +
165B GLN* 1.3 61.2 + - - +
166B VAL* 3.6 5.5 + - + -
184B ARG* 3.3 5.7 - - - -
185B LEU* 2.7 62.4 + - + +
187B LEU* 4.2 9.6 - - + -
240B VAL* 5.7 0.7 - - + -
245B VAL* 4.4 13.7 - - + +
248B ASN* 4.1 15.5 - - - +
249B MET* 3.6 50.4 - - + +
252B THR* 3.7 26.7 - - + -
253B ILE* 4.2 13.5 - - + -
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Residues in contact with GLN 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B TYR* 4.0 15.4 + - + -
91B GLU* 4.4 1.0 - - - +
92B HIS* 3.4 29.2 + - + +
164B TRP* 1.3 73.6 - - - +
166B VAL* 1.3 64.1 + - - +
182B ILE* 3.8 28.9 - - + +
183B TYR 3.6 2.9 - - - -
184B ARG* 2.7 42.9 + - - +
197B LEU* 3.6 7.2 - - - +
239B GLN 4.8 0.2 - - - +
240B VAL* 4.3 9.4 - - - +
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B TRP* 4.0 8.5 - - + +
165B GLN* 1.3 80.8 - - - +
167B ILE* 1.3 64.7 + - - +
168B LEU* 4.4 7.9 - - + +
181B GLY 3.5 0.2 - - - +
182B ILE* 3.5 7.3 - - - +
183B TYR* 2.9 50.1 + - + +
185B LEU* 4.5 8.5 - - + +
194B PHE* 4.7 3.8 - - + -
238B MET* 3.7 39.5 - - + -
239B GLN 3.8 5.4 - - - +
240B VAL* 3.8 17.0 - - + -
249B MET* 4.0 16.2 - - + -
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Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B VAL* 1.3 76.4 - - - +
168B LEU* 1.3 65.9 + - - +
169B LYS* 3.2 23.6 + - + +
181B GLY* 3.2 16.6 - - - +
182B ILE* 3.7 20.9 - - + -
238B MET* 3.1 4.0 - - - -
239B GLN* 2.9 55.6 + - + +
240B VAL* 5.6 2.2 - - - -
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B VAL* 3.8 6.3 - - + -
167B ILE* 1.3 71.3 - - - +
169B LYS* 1.3 61.8 + - - +
174B GLY* 5.9 0.4 - - - -
179B LEU* 3.3 42.6 - - + +
180B ILE* 3.2 9.3 - - - +
181B GLY* 2.7 37.3 + - - +
183B TYR* 3.7 30.7 - - + -
194B PHE* 4.3 18.2 - - + -
236B PHE* 4.0 21.8 - - + -
237B TRP 3.5 15.9 - - - +
238B MET* 4.1 19.5 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il